Jonathan D. Ogata

The paper evaluates exclusion set generation strategies in short-read sequencing, finding that pre-generated Blacklists are hard to reproduce and proposes sponge sequences as an alternative to reduce artifacts.

ShapeUpLMD automates ROI optimization for laser microdissection, improving tumor purity and spatial accuracy in multi-omic tissue profiling.

The paper identifies conserved protein alterations and elevated MUC16 in low-grade serous ovarian cancers through quantitative proteomics and validation across multiple datasets.

The paper provides exclusion region sets for T2T-CHM13, GRCm39, and other genomes through an R/Bioconductor package and API, offering unified access to curated genomic ranges.